E3Docker 2.0

< Back to small molecule database

BDBM513871

E3L021386

Internal ID: BDB021386

Activity data available Local docking-ready structure

Dock with O75530 Dock with Q09028

Structure

/e3_file/ligand_db/generated/BDB021386/BDB021386.sdf

Basic Properties

Compound ID

E3L021386

Internal ID

BDB021386

Molecular formula

C25H23F2N7O

Molecular weight

475.503000

Exact mass

475.193215

XLogP

3.8582

TPSA

91.3700

HBA / HBD

7 / 1

Rotatable bonds

Heavy atoms / rings

35 / 5

Activity summary

IC50 < 100.00000000 nM
10 activity record(s) imported

InChIKey

XMQRHCDCYAICKZ-UHFFFAOYSA-N

SMILES

Cc1c(-c2cnc(NCc3c(F)ccc4c3CCO4)n3cc(C#N)nc23)cnc(CN(C)C)c1F

Aliases

BDBM513871 (preferred) 8-(6-((Dimethylamino)methyl)-5-fluoro-4-methylpyridin-3-yl)-5-(((5-fluoro-2,3-dihydrobenzofuran-4-yl)methyl)amino)imidazo[1,2-c]pyrimidine-2-carbonitrile (source_name) BDBM513871 (source_id)

E3 Relation

E3 UniProt	Gene / protein	Relation type	Ligand role	Direct	Functional	Docking	Source	Evidence
O75530	EED Polycomb protein EED	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM513871	medium ; target=Histone-lysine N-methyltransferase EZH2; Polycomb protein EED
Q09028	RBBP4;RBAP48 Histone-binding protein RBBP4	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM513871	medium ; target=Histone-lysine N-methyltransferase EZH2; Polycomb protein EED

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
BindingDB	BDBM513871	Open	-	10.7270/Q2V69NQ4; 10.7270/Q2J969K9; 10.7270/Q2HQ43R4
PubChem	CID155676957	Open	-

Structure Files

Kind	Format	Status	Docking use	File / link	Preparation note
canonical_2d	SMILES	raw	Docking-ready	Cc1c(-c2cnc(NCc3c(F)ccc4c3CCO4)n3cc(C#N)nc23)cnc(CN(C)C)c1F	keep_bindingdb_unique
generated_3d	SDF	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB021386/BDB021386.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB021386/BDB021386.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB021386/BDB021386.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/BDB021386/BDB021386.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/BDB021386/BDB021386.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
Histone-lysine N-methyltransferase EZH2 O75530 E3 ligase component	BindingDB:BDBM513871	IC50	<100 nM	High	DOI: 10.7270/Q2V69NQ4	1
Histone-lysine N-methyltransferase EZH2 O75530 E3 ligase component	BindingDB:BDBM513871	IC50	<100 nM	High	DOI: 10.7270/Q2J969K9	3 source records
Histone-lysine N-methyltransferase EZH2 Q09028 E3 ligase component	BindingDB:BDBM513871	IC50	<100 nM	High	DOI: 10.7270/Q2J969K9	3 source records
Histone-lysine N-methyltransferase EZH2 Q09028 E3 ligase component	BindingDB:BDBM513871	IC50	<100 nM	High	DOI: 10.7270/Q2V69NQ4	1
Polycomb protein EED Q09028 E3 ligase component	BindingDB:BDBM513871	IC50	<100 nM	High	DOI: 10.7270/Q2HQ43R4	1
Polycomb protein EED O75530 E3 ligase component	BindingDB:BDBM513871	IC50	<100 nM	High	DOI: 10.7270/Q2HQ43R4	1